Habitat suitability assessment and prediction using a physiological species distribution model based on whole-genome genotyping and microclimate data

Microhabitat-scale thermal heterogeneity across sediment burial depths and intraspecific genetic variation are demonstrated to jointly determine habitat suitability for the Manila clam (Ruditapes philippinarum) under climate stress. Heat-tolerant genotypes, identified through cardiac thermal performance assays and genome-wide association analysis of four Chinese coastal populations, gain survival advantages particularly at 5 cm depth where juveniles typically burrow. Temperature simulations revealed pronounced vertical stratification in intertidal flats, with deeper burial (10 cm) providing thermal buffering against extreme heat and creating critical microrefugia. However, extreme summer temperatures reduce habitat suitability for both heat-tolerant and heat-sensitive genotypes, especially in southern China where heat stress is most severe. By integrating genome-wide genetic profiling, physiological traits, and microhabitat temperature data, a physiological species distribution model was developed that highlights the ecological importance of microhabitat variability and intraspecific diversity in coastal systems. These results establish a genotype-microhabitat matching principle governing thermal adaptation in vertically stratified sediments, with implications for sessile species across coastal ecosystems. These findings enhance predictive capacity for benthic species under climate change and inform sustainable management strategies for estuarine and coastal resources.